Methods to Treat Cancer with 10-propargyl-10-deazaaminopterin and Methods for Assessing Cancer for Increased Sensitivity to 10-propargyl-10-deazaaminopterin

ABSTRACT

The present invention relates to a method for assessing the sensitivity of a patient&#39;s cancer to treatment with 10-propargyl-10-deazaaminopterin and a method for selecting a patient for treatment of cancer with 10-propargyl-10-deazaaminopterin, by determining the amount of a selected polypeptide expressed by the cancer and comparing the amount with the amount of the selected polypeptide expressed by a reference cancer, wherein the polypeptide includes a member of folate pathways within cells and may include at least one of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT). The present invention also relates to the use of 10-propargyl-10-deazaaminopterin in the treatment of multiple myeloma.

STATEMENT OF RELATED APPLICATIONS

The present application claims the benefit of U.S. Provisional Application No. 60/869,528, filed Dec. 11, 2006, which application is incorporated herein by reference in its entirety. The present invention claims priority from and is a continuation in part application of pending U.S. Ser. No. 11/568,254, filed Oct. 24, 2006, which is a 371 of PCT/US2005/019170 filed on May 31, 2005, claiming priority to U.S. Ser. No. 60/521,593, filed on May 30, 2004; each of which are incorporated by reference herein in their entireties.

TECHNICAL FIELD

The present invention relates to methods to treat cancer with 10-propargyl-10-deazaaminopterin and methods for assessing cancers and selecting patients for treatment based for increased sensitivity to 10-propargyl-10-deazaaminopterin.

BACKGROUND OF THE INVENTION

10-Propargyl-10-deazaaminopterin (herein “PDX” or “10-propargyl-10dAM” or “pralatrexate”) is a member of a large class of compounds which have been tested and in some cases found useful in the treatment of tumors. This compound, which has the structure shown in FIG. 1, was disclosed by DeGraw et al., “Synthesis and Antitumor Activity of 10-Propargyl-10-deazaaminopterin.” J. Medical Chem. 36: 2228-2231 (1993) and shown to act as an inhibitor of growth in the murine L1210 cell line and to a lesser extent of the enzyme dihydrofolate reductase (“DHFR”). In addition, some results were presented for the antitumor properties of the compound using the E0771 murine mammary tumor model. These data were equivocal because of the small number of mice used in the test (3 per dosage), the absence of any standard deviation information which would quantify the reliability of the data, and the fact that the highest dose used was in fact toxic to the mice. Nevertheless, assuming these data have some predictive value for the efficacy of a drug in treating human tumors, it would at best predict a drug which, at equivalent levels of tolerance, had properties comparable to or perhaps slightly better than nethotrexate.

PCT Publication No. WO98/02163, discloses the surprising observation that more highly purified 10-propargyl-10-dAM compositions when tested in a xenograft model for their efficacy against human tumors have now been shown to be far superior to methotrexate (“MTX”) and are even superior to edatrexate (“ETX”), a more recent clinical candidate. Moreover, 10-propargyl-10dAM showed a surprising ability to cure tumors such that there was no evidence of tumor growth several weeks after the cessation of therapy. Thus, highly purified composition containing 10-propargyl-10dAM. can be used in accordance with the invention to treat tumors, including both solid tumors and leukemias. The composition is illustrated for use in treatment of human mammary tumors and human lung cancer.

Subsequent studies with 10-propargyl-10-dAM have shown that it is useful on its own and in combinations with other therapeutic agents. For example, Sirotnak et al., Clinical Cancer Research Vol. 6, 3705-3712 (2000) reports that co-administration of 10-propargyl-10-dAM and probenecid, an inhibitor of a cMOAT/MRP-like plasma membrane ATPase greatly enhances the efficacy of 10-propargyl-10-dAM against human solid tumors in vivo. 10-propargyl-10-dAM and combinations of 10-propargyl-10-dAM with platinum based chemotherapeutic agents have been shown to be effective against mesothelioma. (Khokar, et al., Clin. Cancer Res. 7: 3199-3205 (2001).

Another subsequent study showed that 10-propargyl-10-dAM has particular utility in the treatment of T-cell lymphomas, even with patients with drug resistant T-cell lymphomas, disclosed in U.S. Patent Publication No. 2005/0267117, which is incorporated by reference herein in its entirety. Other studies have shown a method for assessing sensitivity of a lymphoma to treatment with 10-propargyl-10-dAM by determining the amount of reduced folate carrier-1 enzyme (RFC-1) expressed by the sample, wherein a higher level of expressed RFC-1 is indicative of greater sensitivity to 10-propargyl-10-dAM, disclosed in PCT Publication No. WO 2005/117892, which is incorporated by reference herein in its entirety.

However, a need still remains in the art for determining which other cancers for which 10-propargyl-10-dAM has particular utility in treating, and also for methods for selecting patients for treatment with 10-propargyl-10-dAM, as well as methods for assessing sensitivity of a cancer including lymphoma to 10-propargyl-10-dAM. These and other needs are addressed by the present invention.

The term “lymphomas” refers to a variety of disease states, including Non-Hodgkins Lymphoma (NHL); diffuse large B-cell lymphoma (DLBCL); follicular lymphoma (FL); Hodgkin's Disease; Burkitt's Lymphoma; cutaneous T-cell lymphoma; primary central nervous system lymphoma, and lymphomatous metastases. In most cases, lymphoma is characterized by the presence of cancerous B-cells. However, in T-cell lymphomas, the disease state is characterized by cancerous T-lymphocytes.

All references cited herein, both supra and infra, are hereby incorporated by reference herein in their entireties.

SUMMARY OF THE INVENTION

The present invention relates to a method for assessing the sensitivity of a patient's cancer to treatment with 10-propargyl-10-deazaaminopterin and a method for selecting a patient for treatment of cancer with 10-propargyl-10-deazaaminopterin, by determining the amount of a selected polypeptide expressed by the cancer and comparing the amount with the amount of the selected polypeptide expressed by a reference cancer, wherein the polypeptide includes a member of folate pathways within cells and may include at least one of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT). The present invention also relates to the use of 10-propargyl-10-deazaaminopterin in the treatment of multiple myeloma.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the structure of 10-propargyl-10-dAM and methotrexate;

FIG. 2 shows an HPLC of an impure 10-propargyl-10-dAM preparation prepared in accordance with the prior art;

FIG. 3 shows an HPLC of a highly purified 10-PROPARGYL-10-DAM preparation in accordance with the invention;

FIG. 4 shows a synthetic scheme useful in preparing the compound in accordance with the invention;

FIG. 5( a)-(f) shows a comparison of relative expression of selected folate pathway genes in B- and T-cell lymphoma cell lines; and

FIG. 6( a)-(f) shows a comparison of relative gene expression of selected folate pathway genes during treatment of B-cell (RL) and T-cell (HT) lymphoma cells with 10-propargyl-10-dAM or MTX.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to a method for assessing the sensitivity of a patient's cancer to treatment with 10-propargyl-10-deazaaminopterin and a method for selecting a patient for treatment of cancer with 10-propargyl-10-deazaaminopterin, by determining the amount of a selected polypeptide expressed by the cancer and comparing the amount with the amount of the selected polypeptide expressed by a reference cancer, wherein the polypeptide includes a member of folate pathways within cells and may include at least one of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT). The present invention also relates to the use of 10-propargyl-10-deazaaminopterin in the treatment of multiple myeloma.

As used in the specification and claims of this application, the term “lymphomas” refers to Non-Hodgkins Lymphoma (NHL); diffuse large B-cell lymphoma (DLBCL); follicular lymphoma (FL); Hodgkin's Disease; Burkitt's Lymphoma; cutaneous T-cell lymphoma; primary central nervous system lymphoma, and lymphomatous metastases. In one embodiment of the present invention, this application relates to the use of 10-propargyl-10-deazaaminopterin in the treatment of T-cell lymphoma.

T-cell lymphomas are lymphomas in which the T cells of the patient are determined to be cancerous. T-cell lymphomas encompass a variety of conditions including without limitation: (a) lymphoblastic lymphomas in which the malignancy occurs in primitive lymphoid progenitors from the thymus; (b) mature or peripheral T-cell neoplasms, including T-cell prolymphocytic leukemia, T-cell granular lymphocytic leukemia, aggressive NK-cell leukemia, cutaneous T-cell lymphoma (Mycosis fungoides/Sezary syndrome), anaplastic large cell lymphoma, T-cell type, enteropathy-type T-cell lymphoma, Adult T-cell leukemia/lymphoma including those associated with HTLV-1, and angioimmunoblastic T-cell lymphoma, and subcutaneous panniculitic T-cell lymphoma; and (c) peripheral T-cell lymphomas that initially involve a lymph node paracortex and never grow into a true follicular pattern.

In one embodiment, the present invention includes a method for the treatment of multiple myeloma comprising administering to a patient diagnosed with having multiple myeloma a pharmaceutically acceptable composition comprising a therapeutically effective amount of 10-propargyl-10-deazaaminopterin. In one embodiment, the 10-propargyl-10-deazaaminopterin is substantially free of 10-deazaaminopterin.

In one embodiment of the invention, the composition comprises “highly purified” 10-propargyl-10-dAM. As used in the specification and claims hereof, compositions which are “highly purified” contain 10-propargyl-10-dAM substantially free of other folic acid derivatives, particularly 10-deazaaminopterin, which can interfere with the antitumor activity of the 10-propargyl-10-dAM. A composition within the scope of the invention may include carriers or excipients for formulating the 10-propargyl-10-dAM into a suitable dosage unit form for therapeutic use, as well as additional, non-folate therapeutic agents.

10-propargyl-10-dAM can be synthesized using the method disclosed in the DeGraw paper, supra or in Example 7 of U.S. Pat. No. 5,354,751, which is incorporated herein by reference. HPLC evaluation of the product prepared by this method shows the presence of a substantial amount (about 4.6%) of an impurity A (FIG. 2) which has a retention time consistent with 10-deazaaminopterin. Thus, if this synthetic approach is employed further purification is necessary beyond that disclosed in the DeGraw et al. paper. Such purification can be carried out by additional HPLC or crystallization to remove the 10-deazaaminopterin and other folic acid derivatives which may be present.

For use in the present invention, 10-propargyl-10-dAM is advantageously formulated as part of a pharmaceutical preparation. The specific dosage form will depend on the method of administration, but may include tablets, capsules, oral liquids, and injectable solutions for intravenous, intramuscular or intraperitoneal administration. One suitable dosing schedule involves the administration of 150 mg/m² every two weeks. Lower doses may of course be indicated depending on the tolerance of an individual patient, or if more frequent administration were adopted. For example, doses on the order of 40 to 120 mg/m² of body surface area/day are appropriate. Dosages of 30 mg/m² weekly for 3 weeks followed by a one week rest, 30 mg/m² weekly×6 weeks followed by a one week rest, or gradually increasing doses of 10-propargyl-10-dAM on the weekly×6 week schedule are also suitable. Higher doses could be utilized if less frequent administration were used. Thus, in a general sense, dosages of 30 to 275 mg/m² are suitably used with various dosing schedules, for example 135 to 275 mg/m² for biweekly dosages, and 30 to 150 mg/m² for weekly dosages. The determination of suitable dosages using protocols similar to those described in U.S. Pat. No. 6,323,205, which is incorporated herein by reference, is within the skill in the art. In one embodiment, the 10-propargyl-10-deazaaminopterin is administered in an amount of from about 30 to about 275 mg/m² per dose. Methods of the present invention also include administration of 10-propargyl-10-deazaaminopterin weekly; administration of 10-propargyl-10-deazaaminopterin in a dose of about 30 mg/m²; administration of 10-propargyl-10-deazaaminopterin in an amount of from about 30 to about 150 mg/m² per dose; administration of 10-propargyl-10-deazaaminopterin biweekly; and/or administering 10-propargyl-10-deazaaminopterin in a dosage amount of about 135 to about 275 mg/m².

10-propargyl-10-dAM may be used in combinations with other cytotoxic and antitumor compounds, including vinca alkaloids such as vinblastine, navelbine, and vindesine; probenicid, nucleotide analogs such as gemcitabine, 5-fluorouracil, and cytarabine; alkylating agents such as cyclophosphamide or ifosfamide; cisplatin or carboplatin; leucovorin; taxanes such a paclitaxel or docetaxel; anti-CD20 monoclonal antibodies, with or without radioisotopes, and antibiotics such as doxorubicin and mitomycin. Combinations of 10-propargyl-10-dAM with several of these other antitumor agents or with growth factor inhibitors and anti-angiogenic agents may also be used.

10-propargyl-10-dAM and other agents may be concurrently administered or utilized in combination as part of a common treatment regimen, in which the 10-propargyl-10-dAM and the other agent(s) are administered at different times. For example, the other agent may be administered before, immediately afterward or after a period of time (for example 24 hours) relative to the 10-propargyl-10-dAM administration. Thus, for purposes of this application, the term administering refers generally to concurrent administration or to sequential administration of the drugs and in either order in a parallel treatment regimen with or without a separation in time between the drugs unless otherwise specified.

10-propargyl-10-dAM is suitably used in combination with folic acid and vitamin B12 supplementation to reduce the side effects of the treatment. For example, patients may be treated with folic acid (1 mg/m² daily starting 1 week prior to treatment with 10-propargyl-10-dAM, or alternatively 1 mg perioral (p.o.) daily not based on body surface area (BSA)); and B12 (1 mg/m² monthly, or alternatively given intramuscularly (I.M.) every 8-10 weeks as 1 mg (not based on BSA), or alternatively p.o. daily 1 mg (not based on BSA)).

One embodiment of the present invention includes a method for assessing the sensitivity of a patient's cancer to treatment with 10-propargyl-10-deazaaminopterin. This method includes the following steps, in any order. One step includes obtaining a sample of the patient's cancer tissue. Another step includes determining the amount of at least one selected polypeptide expressed by the sample. Another step includes obtaining a reference expression level for the at least one selected polypeptide for a cancer having sensitivity to 10-propargyl-10-deazaaminopterin. Another step includes comparing the expression data for the at least one selected polypeptide with the reference expression for the at least one selected polypeptide. A match of the sample expression level of the at least one selected polypeptide to the reference expression level of the at least one selected polypeptide indicates the patient's cancer has increased sensitivity to 10-propargyl-10-deazaaminopterin. Another step includes generating a report of the sensitivity of the sample to 10-propargyl-10-deazaaminopterin. A report may be, without limitation, an oral report, a printed report, or an electronically transmitted report. Selected polypeptides include enzymes of any folate pathway in the cell and includes the polypeptides reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH) (also known as folypolyglutamate hydrolase (FPGH)), folylpoly-gamma-glutamate synthetase (FPGS), and glycinamide ribonucleotide formyltransferase (GARFT). Selected polypeptides are also variously referred to herein as “biomarkers of the invention.”

Several proteins are implicated in the metabolism of folic acid and for the targets of anti-folates such as 10-propargyl-10-dAM and MTX in tumor cells. In most tumor cells, the protein encoded by RFC-1 mediates internalization of folate analogs. Once inside the cell, these analogs either bind dihydrofolate reductase (DHFR), thereby depleting intracellular reduced folate pools needed for purine and thymidine biosynthesis, or will be metabolized to a polyglutamate prior to binding to DHFR. Polyglutamylation is catalyzed by FPGS. FPGH (also known as GGH) mediates cleavage and clearance of these intracellular polyglutamated anti-folates. TS and GARFT are also involved in folate metabolism as “recycling” enzymes (thus directly affecting pools of nucleotides available for DNA synthesis). Without intending to be bound by a specific mechanism, it is believed that this correlation between RFC-1 expression levels and 10-propargyl-10-dAM sensitivity is a reflection of increased transport of 10-propargyl-10-dAM into tumor cells. Without being bound by theory, it is believed that alterations in other folate pathway enzymes discussed herein also correlate with 10-propargyl-10-dAM sensitivity; such as, for example, reduced DHFR levels correlating with a decrease in the amount of intracellular drug required to inhibit this enzyme, reduced GARFT and TS potentially reducing the pools of available nucleotides, increased FPGS increasing the rate of polyglutamylation of 10-propargyl-10-dAM and resulting in increased retention within the cell to facilitate ongoing activity against DHFR.

In another embodiment of the present invention, a method of selecting a patient for treatment of a cancer with 10-propargyl-10-deazaaminopterin is provided. The method includes the following steps, in any order. One step includes obtaining a sample of the patient's cancer tissue. Another step includes determining the amount of at least one selected polypeptide expressed by the sample. Another step includes obtaining a reference expression level for the at least one selected polypeptide for a cancer having sensitivity to 10-propargyl-10-deazaaminopterin. Another step includes comparing the expression data for the at least one selected polypeptide with the reference expression for the at least one selected polypeptide. A match of the sample expression level of the at least one selected polypeptide to the reference expression level of the at least one selected polypeptide indicates the patient's cancer has increased sensitivity to 10-propargyl-10-deazaaminopterin. Selected polypeptides include reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH) (also known as folypolyglutamate hydrolase (FPGH)), folylpoly-gamma-glutamate synthetase (FPGS), and glycinamide ribonucleotide formyltransferase (GARFT). Another step includes selecting the patient for treatment 10-propargyl-10-deazaaminopterin when the expression of the sample protein and the reference protein matches.

As used herein, the terms “protein” and “polypeptide” and “proteinaceous agent” are used interchangeably to refer to a chain of amino acids linked together by peptide bonds which optionally can comprise natural or non-natural amino acids. Optionally, the protein or peptide can comprise other molecules in addition to amino acids. Said chain can be of any length. Polypeptides of the present invention include enzymes related to folate pathways in cells including the selected polypeptides, including reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH) (also known as folypolyglutamate hydrolase (FPGH)), folylpoly-gamma-glutamate synthetase (FPGS), and glycinamide ribonucleotide formyltransferase (GARFT). The accession numbers and SEQ ID NOs of the selected polypeptides are as follows:

GenBank Poly- Accession SEQ ID peptide Full name Number NOs DHFR dihydrofolate reductase NM_000791 4, 5, 6 FPGS folylpolyglutamate synthetase M98045 13, 14, 15 GARFT glycinamide ribonucleotide X54199 16, 17, 18 transformylase GGH gamma-glutamyl hydrolase NM_003878 10, 11, 12 RFC-1 reduced folate carrier, member 1 NM_194255.1 1, 2, 3 TS Thymidylate synthase NM_001071 7, 8, 9

As used herein, nucleotide sequences of the gene products of the above identified selected polypeptides include, but are not limited to, the cDNA, genome-derived DNA and synthetic or semi-synthetic DNA or RNA. The full length gene nucleotide sequence of RFC-1 is contained in SEQ. ID. NO: 1; the full length gene nucleotide sequence of DHFR is contained in SEQ. ID. NO: 4, the full length gene nucleotide sequence of TS is contained in SEQ. ID. NO: 7, the full length gene nucleotide sequence of GGH is contained in SEQ. ID. NO: 10, the full length gene nucleotide sequence of FPGH is contained in SEQ. ID. NO: 13, and the full length gene nucleotide sequence of GARFT is contained in SEQ. ID. NO: 16.

The term “polynucleotide” is used to mean a polymeric form of nucleotides of any length, which contain deoxyribonucleotides, ribonucleotides, and/or their analogs. The terms “polynucleotide” and “nucleotide” as used herein are used interchangeably. Polynucleotides can have any three-dimensional structure, and can perform any function, known or unknown. The term “polynucleotide” includes double-stranded, single-stranded, and triple-helical molecules. Unless otherwise specified or required, any embodiment of the invention described herein that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double stranded form.

The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide can be comprised of modified nucleotides, such as methylated nucleotides and nucleotide analogs. Analogs of purines and pyrimidines are known in the art, and include, but are not limited to, aziridinylcytosine, 4-acetylcytosine, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, pseudouracil, 5-pentynyluracil and 2,6-diaminopurine. The use of uracil as a substitute for thymine in a deoxyribonucleic acid is also considered an analogous form of pyrimidine.

A “fragment” (also called a “region”) of a polynucleotide (i.e., a polynucleotide encoding a sarp) is a polynucleotide comprised of at least 9 contiguous nucleotides of the novel genes. Preferred fragments are comprised of a region encoding at least 5 contiguous amino acid residues, more preferably, at least 10 contiguous amino acid residues, and even more preferably at least 15 contiguous amino acid residues.

The term “recombinant” polynucleotide as used herein intends a polynucleotide of genomic, cDNA, semisynthetic, or synthetic in origin which, by virtue of its origin or manipulation: is not associated with all or a portion of a polynucleotide with which it is associated in nature; is linked to a polynucleotide other than that to which it is linked in nature; or does not occur in nature.

As used herein, reference to a selected gene product, protein or polypeptide in the present invention, including RFC-1 (SEQ ID NO:3), DHFR (SEQ ID NO:6), TS (SEQ ID NO:9), GGH, (also known as FPGH) (SEQ ID NO:12), FPGS (SEQ ID NO:15), and GARFT (SEQ ID NO:18), includes full-length proteins, fusion proteins, or any fragment or homologue of such a protein. The amino acid sequence for RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT from human are described herein as exemplary folate metabolism associated polypeptides and proteins. In addition, and by way of example, a “human RFC-1, DH FR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein” refers to a RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein (generally including a homologue of a naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein) from a human (Homo sapiens) or to a RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein that has been otherwise produced from the knowledge of the structure (e.g., sequence) and perhaps the function of a naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein from Homo sapiens. In other words, a human RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein includes any RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein that has substantially similar structure and function of a naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein from Homo sapiens or that is a biologically active (i.e., has biological activity) homologue of a naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein from Homo sapiens as described in detail herein. As such, a human RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein can include purified, partially purified, recombinant, mutated/modified and synthetic proteins. According to the present invention, the terms “modification” and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the amino acid sequence of RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT (or nucleic acid sequences) described herein.

As used herein, the term “homologue” is used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the “prototype” or “wild-type” protein) by minor modifications to the naturally occurring protein or peptide, but which maintains the basic protein and side chain structure of the naturally occurring form. Such changes include, but are not limited to: changes in one or a few amino acid side chains; changes one or a few amino acids, including deletions (e.g., a truncated version of the protein or peptide) insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: methylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, amidation and/or addition of glycosylphosphatidyl inositol. A homologue can have either enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide. A homologue can include an agonist of a protein or an antagonist of a protein.

Homologues can be the result of natural allelic variation or natural mutation. A naturally occurring allelic variant of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code. Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.

Homologues can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.

According to the present invention, an isolated RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein, including a biologically active homologue or fragment thereof, has at least one characteristic of biological activity of activity a wild-type, or naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT protein (which can vary depending on whether the homologue or fragment is an agonist, antagonist, or mimic of RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT, and the isoform of RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT).

Homologues of RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT, including peptide and non-peptide agonists and antagonists of RFC-1, DH FR, TS, GGH, (also known as FPGH), FPGS, and GARFT (analogues), can be products of drug design or selection and can be produced using various methods known in the art. Such homologues can be referred to as mimetics.

In one embodiment, a RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT homologue comprises, consists essentially of, or consists of, an amino acid sequence that is at least about 45%, or at least about 50%, or at least about 55%, or at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95% identical, or at least about 95% identical, or at least about 96% identical, or at least about 97% identical, or at least about 98% identical, or at least about 99% identical (or any percent identity between 45% and 99%, in whole integer increments), to a naturally occurring RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT amino acid sequence. A homologue of RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT differs from a reference (e.g., wild-type) RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT and therefore is less than 100% identical to the reference RFC-1, DHFR, TS, GGH, (also known as FPGH), FPGS, and GARFT at the amino acid level.

As used herein, unless otherwise specified, reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches and blastn for nucleic acid searches with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S. F., Madden, T. L., Sch{umlaut over (aa)}ffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25:3389-3402, incorporated herein by reference in its entirety); (2) a BLAST 2 alignment (using the parameters described below); (3) and/or PSI-BLAST with the standard default parameters (Position-Specific Iterated BLAST. It is noted that due to some differences in the standard parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences might be recognized as having significant homology using the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic BLAST using one of the sequences as the query sequence may not identify the second sequence in the top matches. In addition, PSI-BLAST provides an automated, easy-to-use version of a “profile” search, which is a sensitive way to look for sequence homologues. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using any one of these programs.

The term, “primer”, as used herein refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a DNA polymerase and at a suitable temperature and pH. The primer may be either single-stranded or double-stranded and must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon many factors, including temperature, source of primer and the method used. For example, for diagnostic applications, depending on the complexity of the target sequence, the oligonucleotide primer typically contains 15-25 or more nucleotides, although it may contain fewer nucleotides. The factors involved in determining the appropriate length of primer are readily known to one of ordinary skill in the art. In general, the design and selection of primers embodied by the instant invention is according to methods that are standard and well known in the art, see Dieffenbach, C. W., Lowe, T. M. J., Dveksler, G. S. (1995) General Concepts for PCR Primer Design. In: PCR Primer, A Laboratory Manual (Eds. Dieffenbach, C. W, and Dveksler, G. S.) Cold Spring Harbor Laboratory Press, New York, 133-155; Innis, M. A., and Gelfand, D. H. (1990) Optimization of PCRs. In: PCR protocols, A Guide to Methods and Applications (Eds. Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J.) Academic Press, San Diego, 3-12; Sharrocks, A. D. (1994) The design of primers for PCR. In: PCR Technology, Current Innovations (Eds. Griffin, H. G., and Griffin, A. M, Ed.) CRC Press, London, 5-11.

As used herein, the terms “RNA portion” and “a portion thereof” in context of RNA products of a biomarker of the invention refer to an RNA transcript comprising a nucleic acid sequence of at least 6, at least 9, at least 15, at least 18, at least 21, at least 24, at least 30, at least 60, at least 90, at least 99, or at least 108, or more nucleotides of a RNA product of a biomarker of the invention.

Obtaining a sample of the patient's cancer tissue may be done by any methods known in the art. Bone marrow or lymph node biopsies and analysis of peripheral blood samples for cytogenetic and/or immunologic analysis is standard practice. Frozen tissue specimens may be obtained as well. As used herein a “sample” can be from any organism and can further include, but is not limited to, peripheral blood, plasma, urine, saliva, gastric secretion, feces, bone marrow specimens, primary tumors, metastatic tissue, embedded tissue sections, frozen tissue sections, cell preparations, cytological preparations, exfoliate samples (e.g., sputum), fine needle aspirations, amino cells, fresh tissue, dry tissue, and cultured cells or tissue. It is further contemplated that the biological sample of this invention can also be whole cells or cell organelles (e.g., nuclei). The sample can be unfixed or fixed according to standard protocols widely available in the art.

In some embodiments of the present invention, peripheral blood is drawn, or alternatively, if desired, leukocytes may be isolated by differential gradient separation, using, for example, ficoll-hypaque or sucrose gradient solutions for cell separations, followed by ammonium chloride or hypotonic lysis of remaining contaminating erythrocytes (“Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds)). Bone marrow and lymph node biopsies may be processed by collagenase/dispase treatment of the biopsy material, or by homogenization in order to obtain single cell suspensions (“Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds)).

The sample can be from a subject or a patient. As utilized herein, the “subject” or “patient” of the methods described herein can be any animal. In a preferred embodiment, the animal of the present invention is a human. In addition, determination of expression patterns is also contemplated for non-human animals which can include, but are not limited to, cats, dogs, birds, horses, cows, goats, sheep, guinea pigs, hamsters, gerbils, mice and rabbits.

The term “cancer,” or “reference cancer”, when used herein refers to or describes the pathological condition, preferably in a mammalian subject, that is typically characterized by unregulated cell growth. Non-limiting cancer types include carcinoma (e.g., adenocarcinoma), sarcoma, myeloma, leukemia, and lymphoma, and mixed types of cancers, such as adenosquamous carcinoma, mixed mesodermal tumor, carcinosarcoma, and teratocarcinoma. Representative cancers include, but are not limited to, bladder cancer, lung cancer, including NSCLC. Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. It usually grows and spreads more slowly than small cell lung cancer. There are three forms of NSCLC: Adenocarcinomas are often found in an outer area of the lung. Squamous cell carcinomas are usually found in the center of the lung by an air tube (bronchus). Large cell carcinomas can occur in any part of the lung. Other cancers include breast cancer, colon cancer, rectal cancer, endometrial cancer, ovarian cancer; head and neck cancer, prostate cancer, and melanoma. Specifically included are AIDS-related cancers (e.g., Kaposi's Sarcoma, AIDS-related lymphoma), bone cancers (e.g., osteosarcoma, malignant fibrous histiocytoma of bone, Ewing's Sarcoma, and related cancers), and hematologic/blood cancers (e.g., adult acute lymphoblastic leukemia, childhood acute lymphoblastic leukemia, adult acute myeloid leukemia, childhood acute myeloid leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, hairy cell leukemia, adult Hodgkin's disease, childhood Hodgkin's disease, Hodgkin's disease during pregnancy, adult non-Hodgkin's lymphoma, childhood non-Hodgkin's lymphoma, non-Hodgkin's lymphoma during pregnancy, primary central nervous system lymphoma, Waldenstrom's macroglobulinemia, multiple myeloma/plasmacell neoplasm, myelodysplastic syndrome, and myeloproliferative disorders), as well as lymphoblastic lymphomas in which the malignancy occurs in primitive lymphoid progenitors from the thymus; mature or peripheral T-cell neoplasms, including T-cell prolymphocytic leukemia, T-cell granular lymphocytic leukemia, aggressive NK-cell leukemia, cutaneous T-cell lymphoma (Mycosis fungoides/Sezary syndrome), anaplastic large cell lymphoma, T-cell type, enteropathy-type T-cell lymphoma, Adult T-cell leukemia/lymphoma including those associated with HTLV-1, and angioimmunoblastic T-cell lymphoma, and subcutaneous panniculitic T-cell lymphoma; and peripheral T-cell lymphomas that initially involve a lymph node paracortex and never grow into a true follicular pattern.

Also included are brain cancers (e.g., adult brain tumor, childhood brain stem glioma, childhood cerebellar astrocytoma, childhood cerebral astrocytoma, childhood ependymoma, childhood medulloblastoma, supratentorial primitive neuroectodermal and pineal, and childhood visual pathway and hypothalamic glioma), digestive/gastrointestinal cancers (e.g., anal cancer, extrahepatic bile duct cancer, gastrointestinal carcinoid tumor, colon cancer, esophageal cancer, gallbladder cancer, adult primary liver cancer, childhood liver cancer, pancreatic cancer, rectal cancer, small intestine cancer, and gastric cancer), musculoskeletal cancers (e.g., childhood rhabdomyosarcoma, adult soft tissue sarcoma, childhood soft tissue sarcoma, and uterine sarcoma), and endocrine cancers (e.g., adrenocortical carcinoma, gastrointestinal carcinoid tumor, islet cell carcinoma (endocrine pancreas), parathyroid cancer, pheochromocytoma, pituitary tumor, and thyroid cancer).

Also included are neurologic cancers (e.g., neuroblastoma, pituitary tumor, and primary central nervous system lymphoma), eye cancers (e.g., intraocular melanoma and retinoblastoma), genitourinary cancers (e.g., bladder cancer, kidney (renal cell) cancer, penile cancer, transitional cell renal pelvis and ureter cancer, testicular cancer, urethral cancer, Wilms' tumor and other childhood kidney tumors), respiratory/thoracic cancers (e.g., non-small cell lung cancer, small cell lung cancer, malignant mesothelioma, and malignant thymoma), germ cell cancers (e.g., childhood extracranial germ cell tumor and extragonadal germ cell tumor), skin cancers (e.g., melanoma, and merkel cell carcinoma), gynecologic cancers (e.g., cervical cancer, endometrial cancer, gestational trophoblastic tumor, ovarian epithelial cancer, ovarian germ cell tumor, ovarian low malignant potential tumor, uterine sarcoma, vaginal cancer, and vulvar cancer), and unknown primary cancers.

In one embodiment, the cancer is a lymphoma. In another embodiment, the cancer is a T-cell lymphoma. In yet another embodiment, the cancer is a multiple myeloma. In one embodiment, the sample and the reference cancer are both the same cancer sub-type, i.e., the sample cancer is derived from the same type of cell as the reference cancer. In another embodiment, the reference cancer is any one of or a combination of a cancer or cancerous cell line derived from a T-cell lymphoma or a multiple myeloma, such as, for example, lymphoblastic lymphomas in which the malignancy occurs in primitive lymphoid progenitors from the thymus; mature or peripheral T-cell neoplasms, including T-cell prolymphocytic leukemia, T-cell granular lymphocytic leukemia, aggressive NK-cell leukemia, cutaneous T-cell lymphoma (Mycosis fungoides/Sezary syndrome), anaplastic large cell lymphoma, T-cell type, enteropathy-type T-cell lymphoma, Adult T-cell leukemia/lymphoma including those associated with HTLV-1, and angioimmunoblastic T-cell lymphoma, and subcutaneous panniculitic T-cell lymphoma; and peripheral T-cell lymphomas that initially involve a lymph node paracortex.

In another embodiment of the present invention, the reference cancer or cancerous cell line is a reference cancer or cancerous cell line which is known to have a greater sensitivity to 10-propargyl-10-dAM. The term, “greater sensitivity,” includes those cancers that are known or are found to have an enhanced response to 10-propargyl-10-dAM as compared to MTX. Increased sensitivity may be determined by those of skill in the art and may include assessment of effects seen in cell lines derived from that cancer and/or type of cancer, in animal models, such as mouse subcutaneous transplantation models, and therapeutic indicators such as remission or other indicia of reduced tumor burden in patients, such as increased apoptosis, decreased tumor volume, growth inhibition, and other indicia known to those in the art. An enhanced response can include differential effects seen at equivalent doses of, serum concentrations of, or other indicia of equivalence between, MDX and 10-propargyl-10-dAM.

The selected polypeptides may be quantitated and/or relative amounts determined by any method known in the art for quantitating and/or determining relative amounts of expression levels. The term, “quantitate” or “quantitation” also includes determination of relative amounts of a polypeptide or its transcript. Quantitating transcript RNA or portions thereof of a selected polypeptide is one such method. RNA may be extracted from biological samples via a number of standard techniques (see Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989)). Guanidium-based methods for cell lysis enabling RNA isolation, with subsequent cesium chloride step gradients for separation of the RNA from other cellular macromolecules, followed by RNA precipitation and resuspension, is an older, less commonly employed method of RNA isolation (Glisin, Ve. et al (1973) Biochemistry 13: 2633). Alternatively, RNA may be isolated in a single step procedure (U.S. Pat. No. 4,843,155, and Puissant, C. and Houdebine L. M. (1990) Biotechniques 8: 148-149). Single step procedures include the use of Guanidium isothiocyanate for RNA extraction, and subsequent phenol/chloroform/isoamyl alcohol extractions facilitating the separation of total RNA from other cellular proteins and DNA. Commercially available single-step formulations based on the above-cited principles may be employed, including, for example, the use of the TRIZOL reagent (Life Technologies, Gaithersburg, Md.).

According to further features of preferred embodiments of the present invention, monitoring selected polypeptide RNA/gene expression is via a number of standard techniques well described in the art, any of which can be employed to evaluate selected polypeptide expression. These assays comprise Northern blot and dot blot analysis, primer extension, RNase protection, RT-PCR, in-situ hybridization and chip hybridization. Specific selected polypeptide RNA sequences can be readily detected by hybridization of labeled probes to blotted RNA preparations extracted as above. In Northern blot analysis, fractionated RNA is subjected to denaturing agarose gel electrophoresis, which prevents RNA from assuming secondary structures that might inhibit size based separation. RNA is then transferred by capillary transfer to a nylon or nitrocellulose membrane support and may be probed with a labeled oligonucleotide probe complementary to the selected polypeptide sequence (Alwine, et al. (1977). Proc. Natl. Acad. Sci. USA 74: 5350-5354 and Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989)).

Alternatively, unfractionated RNA may be immobilized on a nylon or nitrocellulose membrane, and similarly probed for selected polypeptide-specific expression, by Slot/Dot blot analysis. RNA slot/dot blots can be prepared by hand, or alternatively constructed using a manifold apparatus, which facilitates comparing hybridization signals by densitometry scanning (Chomczynski P. (1992) Anal. Biochem. 201: 134-139). Primer extension is an additional means whereby quantification of the RNA may be accomplished. Primer extension provides an additional benefit in mapping the 5′ terminus of a particular RNA, by extending a primer using the enzyme reverse transcriptase. In this case, the primer is an oligonucleotide (or restriction fragment) complementary to a portion of the selected polypeptide mRNA. The primer is end-labeled, and is allowed to hybridize to template selected polypeptide mRNA. Once hybridized, the primer is extended by addition of reverse transcriptase, and incorporation of unlabeled deoxynucleotides to for a single-stranded DNA complementary to template selected polypeptide mRNA. DNA is then analyzed on a sequencing gel, with the length of extended primer serving to map the 5′ position of the mRNA, and the yield of extended product reflecting the abundance of RNA in the sample (Jones et al (1985) Cell 42: 559-572 and Micrendorf R. C. And Pfeffer, D. (1987). Methods Enzymol. 152: 563-566).

RNase protection assays provide a highly sensitive means of quantifying selected polypeptide RNA, even in low abundance. In protection assays, sequence-specific hybridization of ribonucleotide probes complementary to selected polypeptide RNA, with high specific activity are generated, and hybridized to sample RNA. Hybridization reactions are then treated with ribonuclease to remove free probe, leaving intact fragments of annealed probe hybridized to homologous selected polypeptide sequences in sample RNA. Fragments are then analyzed by electrophoresis on a sequencing gel, when appropriately-sized probe fragments are visualized (Zinn K. et al (1983) Cell 34: 865-879 and Melton S. A., et al (1984). Nucl. Acids Res. 12: 7035-7056).

RT-PCR is another means by which selected polypeptide expression is verified. RT-PCR is a particularly useful method for detecting rare transcripts, or transcripts in low abundance. RT-PCR employs the use of the enzyme reverse transcriptase to prepare cDNA from RNA samples, using deoxynucleotide primers complementary to the selected polypeptide mRNA. Once the cDNA is generated, it is amplified through the polymerase chain reaction, by the addition of deoxynucleotides and a DNA polymerase that functions at high temperatures. Through repetitive cycles of primer annealing, incorporation of deoxynucleotides facilitating cDNA extension, followed by strand denaturation, amplification of the desired sequence occurs, yielding an appropriately sized fragment that may be detected by agarose gel electrophoresis. Optimal reverse transcription, hybridization, and amplification conditions will vary depending upon the sequence composition and length(s) of the primers and target(s) employed, and the experimental method selected by the practitioner. Various guidelines may be used to select appropriate primer sequences and hybridization conditions (see, e.g., Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, (Volumes 1-3) Cold Spring Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y.).

In-situ hybridization provides another tool for the detection and localization of cell/tissue specific selected polypeptide RNA expression. Labeled anti-sense RNA probes are hybridized to mRNAs in cells singly, or in processed tissue slices, which are immobilized on microscope glass slides (In Situ Hybridization: Medical Applications (eds. G. R. Coulton and J. de Belleroche), Kluwer Academic Publishers, Boston (1992); In Situ Hybridization: In Neurobiology; Advances in Methodology (eds. J. H. Eberwine, K. L. Valentino, and J. D. Barchas), Oxford University Press Inc., England (1994); and In Situ Hybridization: A Practical Approach (ed. D. G. Wilkinson), Oxford University Press Inc., England (1992)). Numerous non-isotopic systems have been developed to visualize labeled DNA probes including; a) fluorescence-based direct detection methods, b) the use of digoxigenin- and biotin-labeled DNA probes coupled with fluorescence detection methods, and c) the use of digoxigenin- and biotin-labeled DNA probes coupled with antibody-enzyme detection methods. When fluorescence-labeled anti-sense RNA probes are hybridized to cellular RNA, the hybridized probes can be viewed directly using a fluorescence microscope. Direct fluorochrome-labeling of the nucleic acid probes eliminate the need for multi-layer detection procedures (e.g., antibody-based-systems), which allows fast processing and also reduces non-specific background signals, hence providing a versatile and highly sensitive means of identifying selected polypeptide gene expression.

Chip hybridization utilizes selected polypeptide-specific oligonucleotides attached to a solid substrate, which may consist of a particulate solid phase such as nylon filters, glass slides or silicon chips [Schena et al. (1995) Science 270:467-470] designed as a microarray. Microarrays are known in the art and consist of a surface to which probes that correspond in sequence to gene products (such as cDNAs) can be specifically hybridized or bound at a known position for the detection of selected polypeptide gene expression. Quantification of the hybridization complexes is well known in the art and may be achieved by any one of several approaches. These approaches are generally based on the detection of a label or marker, such as any radioactive, fluorescent, biological or enzymatic tags or labels of standard use in the art. A label can be applied to either the oligonucleotide probes or the RNA derived from the biological sample.

In general, mRNA quantification is preferably effected alongside a calibration curve so as to enable accurate mRNA determination. Furthermore, quantifying transcript(s) originating from a biological sample is preferably effected by comparison to a normal sample, which sample is characterized by normal expression pattern of the examined transcript(s).

Selected polypeptide expression may also be evaluated at the level of protein expression, either by demonstration of the presence of the protein, or by its activity, with activity herein referring to the enzymatic activity of the selected polypeptide enzyme. Methods for monitoring specific polypeptide protein expression include the following methods discussed below. Anti-selected polypeptide-antibodies for use in selected polypeptide-specific protein detection are readily generated by methods known in the art and include both polyclonal and monoclonal antibodies. The antibodies preferably bind to both native and denatured selected polypeptides and may be detected by several well-known assays in the art, including ELISA, RIA, light emission immunoassays, Western blot analysis, immunofluorescence assays, immunohistochemistry and FACS analysis.

Enzyme linked immunosorbant (ELISA) assays and radioimmunoassays (RIA) follow similar principles for detection of specific antigens, in this case, selected polypeptides. In RIA a selected polypeptide-specific antibody is radioactively labeled, typically with ¹²⁵I. In ELISA assays a selected polypeptide-specific antibody is chemically linked to an enzyme. Selected polypeptide-specific capturing antibody is immobilized onto a solid support. Unlabelled specimens, e.g., protein extracts from biopsy or blood samples are then incubated with the immobilized antibody under conditions where non-specific binding is blocked, and unbound antibody and/or protein removed by washing. Bound selected polypeptide is detected by a second selected polypeptide-specific labeled antibody. Antibody binding is measured directly in RIA by measuring radioactivity, while in ELISA binding is detected by a reaction converting a colorless substrate into a colored reaction product, as a function of linked-enzyme activity. Changes can thus readily be detected by spectrophotometry (Janeway C. A. et al (1997). “Immunbiology” 3rd Edition, Current Biology Ltd., Garland Publishing Inc.; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds)). Both assays therefore provide a means of quantification of selected polypeptide protein content in a biological sample.

Selected polypeptide protein expression may also be detected via light emission immunoassays. Much like ELISA and RIA, in light emission immunoassays the biological sample/protein extract to be tested is immobilized on a solid support, and probed with a specific label, labeled anti-selected polypeptide antibody. The label, in turn, is luminescent, and emits light upon binding, as an indication of specific recognition. Luminescent labels include substances that emit light upon activation by electromagnetic radiation, electro chemical excitation, or chemical activation and may include fluorescent and phosphorescent substances, scintillators, and chemiluminescent substances. The label can be a part of a catalytic reaction system such as enzymes, enzyme fragments, enzyme substrates, enzyme inhibitors, coenzymes, or catalysts; part of a chromogen system such as fluorophores, dyes, chemiluminescers, luminescers, or sensitizers; a dispersible particle that can be non-magnetic or magnetic, a solid support, a liposome, a ligand, a receptor, a hapten radioactive isotope, and so forth (U.S. Pat. No. 6,410,696, U.S. Pat. No. 4,652,533 and European Patent Application No. 0,345,776), and provide an additional, highly sensitive method for detection of selected polypeptide protein expression.

Western blot analysis is another means of assessing selected polypeptide content in a biological sample. Protein extracts from biological samples of, for example, hematopoietic cells, are solubilized in a denaturing ionizing environment, and aliquots are applied to polyacrylamide gel matrixes. Proteins separate based on molecular size properties as they migrate toward the anode. Antigens are then transferred to nitrocellulose, PVDF or nylon membranes, followed by membrane blocking to minimize non-specific binding. Membranes are probed with antibodies directly coupled to a detectable moiety, or are subsequently probed with a secondary antibody containing the detectable moiety. Typically the enzymes horseradish peroxidase or alkaline phosphatase are coupled to the antibodies, and chromogenic or luminescent substrates are used to visualize activity (Harlow E. et al (1998) Immunoblotting. In Antibodies: A Laboratory Manual, pp. 471-510 CSH Laboratory, cold Spring Harbor, N.Y. and Bronstein I. Et al. (1992) Biotechniques 12: 748-753). Unlike RIA, ELISA, light emission immunoassays and immunblotting, which quantify selected polypeptide content in whole samples, immunofluorescence/immunocytochemistry may be used to detect proteins in a cell-specific manner, though quantification is compromised.

In some steps of the methods of the present invention, the level of expression of the RNA and/or protein products of one or more biomarkers of the invention, as measured by the amount or level of RNA or protein, is compared to see if the level of expression “matches.” The term “match” indicates that the level of expression of mRNA, and/or one or more spliced variants of mRNA of the biomarker in the sample is compared with the level of expression of the same one or more biomarkers of the invention as measured by the amount or level of RNA, including mRNA and/or one or more spliced variants of mRNA in a reference sample, and is determined to be similar, for example, by one of skill in the art and/or in accordance with the discussion hereinbelow. A “match” can also include a measurement of the protein, or one or more protein variants encoded by the biomarker of the invention in the sample as compared with the amount or level of protein expression, including one or more protein variants of the biomarker or biomarkers of the invention in the reference sample. A match may be determined by comparing a first population of samples as compared with a second population of samples or a single sample to a reference using either a ratio of the level of expression or using p-value. When using p-value, a nucleic acid transcript including hnRNA and mRNA is identified as being differentially expressed as between a first and second population when the p-value is less than 0.1, less than 0.05, less than 0.01, less than 0.005, less than 0.001 etc. A “match” indicating that the level of expression of the biomarker or selected polypeptide of the sample or population of samples is similar to the level of expression of the biomarker or selected polypeptide of the reference may be determined by one of skill in the art, and includes a level of expression in the sample that is at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 98%, at least about 100%, at least about 110%, at least about 120%, at least about 130%, at least about 140%, at least about 150%, at least about 160%, at least about 170%, at least about 180%, at least about 200%, at least about three fold, at least about four fold, at least about five fold, at least about ten fold, of the reference.

In another embodiment, the present invention includes a method to modulate the expression of a selected polypeptide in a patient's cancer comprising administering to a patient an effective amount of 10-propargyl-10-deazaaminopterin, wherein the selected polypeptide is selected from the group consisting reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH) (also known as folypolyglutamate hydrolase (FPGH)), folylpoly-gamma-glutamate synthetase (FPGS), and glycinamide ribonucleotide formyltransferase (GARFT). A patient's cancer can include any cancer. In one embodiment, the patient's cancer is a lymphoma; in one embodiment, the patient's cancer is a T-cell lymphoma; in another embodiment, the patient's cancer is multiple myeloma. In another embodiment, the patient's cancer is a NSCLC. The modulation can occur in vitro and/or in vivo.

Modulation includes both up-regulation and down-regulation. As used herein, the term “up regulated” or “increased level of expression” in the context of this invention refers to a sequence corresponding to a gene which is expressed wherein the measure of the quantity of the sequence demonstrates an increased level of expression of the gene in the patient as compared to prior to administration of 10-propargyl-10-deazaaminopterin, and can be observed at any point in treatment with 10-propargyl-10-deazaaminopterin. An “increased level of expression” according to the present invention, is an increase in expression of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10% or more, for example, 20%, 30%, 40%, or 50%, 60%, 70%, 80%, 90% or more, or greater than 1-fold, up to 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 50-fold, 100-fold or more. In one embodiment, the polypeptide that is up-regulated is RFC-1 and the cancer is a T-cell lymphoma, multiple myeloma, or a NSCLC.

“Down regulation” or “decreased level of expression” in the context of this invention refers to a sequence corresponding to a gene which is expressed wherein the measure of the quantity of the sequence demonstrates a decreased level of expression of the gene in the patient as compared to prior to administration of 10-propargyl-10-deazaaminopterin, and can be observed at any point in treatment with 10-propargyl-10-deazaaminopterin. A “decreased level of expression” according to the present invention, is a decrease in expression of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10% or more, for example, 20%, 30%, 40%, or 50%, 60%, 70%, 80%, 90% or more, or greater than 1-fold, up to 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 50-fold, 100-fold or more. In one embodiment, the 10-propargyl-10-deazaaminopterin is substantially free of 10-deazaaminopterin. In one embodiment, the modulation is down-regulation, and the downregulation of expression of polypeptide is TS and/or DFHR, and the cancer is NSCLC, T-cell lymphoma, or multiple myeloma.

In one embodiment, kits are provided for measuring a RNA product of a biomarker of the invention which comprise materials and reagents that are necessary for measuring the expression of the RNA product. For example, a microarray or RT-PCR kit may be used and contain only those reagents and materials necessary for measuring the levels of RNA products of any number of up to at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, all or any combination of the biomarkers of the invention. Alternatively, in some embodiments, the kits can comprise materials and reagents that are not limited to those required to measure the levels of RNA products of any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention. For example, a microarray kit may contain reagents and materials necessary for measuring the levels of RNA products any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention, in addition to reagents and materials necessary for measuring the levels of the RNA products of any number of up to at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, or more genes other than the biomarkers of the invention. In a specific embodiment, a microarray or RT-PCR kit contains reagents and materials necessary for measuring the levels of RNA products of any number of up to at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, all or any combination of the biomarkers of the invention, and any number of up to 1, 2, 3, 4, 5, 10 or more genes that are not biomarkers of the invention.

For nucleic acid microarray kits, the kits generally comprise probes attached to a support surface. The probes may be labeled with a detectable label. In a specific embodiment, the probes are specific for the 5′ region, the 3′ region, the internal coding region, an exon(s), an intron(s), an exon junction(s), or an exon-intron junction(s), of any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention. The microarray kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay. The kits may also comprise hybridization reagents and/or reagents necessary for detecting a signal produced when a probe hybridizes to a target nucleic acid sequence. Generally, the materials and reagents for the microarray kits are in one or more containers. Each component of the kit is generally in its own a suitable container.

For RT-PCR kits, the kits generally comprise pre-selected primers specific for particular RNA products (e.g., an exon(s), an intron(s), an exon junction(s), and an exon-intron junction(s)) of any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention. The RT-PCR kits may also comprise enzymes suitable for reverse transcribing and/or amplifying nucleic acids (e.g., polymerases such as Taq), and deoxynucleotides and buffers needed for the reaction mixture for reverse transcription and amplification. The RT-PCR kits may also comprise probes specific for any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention. The probes may or may not be labeled with a detectable label (e.g., a fluorescent label). Each component of the RT-PCR kit is generally in its own suitable container. Thus, these kits generally comprise distinct containers suitable for each individual reagent, enzyme, primer and probe. Further, the RT-PCR kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.

For antibody based kits, the kit can comprise, for example: (1) a first antibody (which may or may not be attached to a support) which binds to protein of interest (e.g., a protein product of any number of up to 1, 2, 3, 4, 5, 6, all or any combination of the biomarkers of the invention); and, optionally, (2) a second, different antibody which binds to either the protein, or the first antibody and is conjugated to a detectable label (e.g., a fluorescent label, radioactive isotope or enzyme). The antibody-based kits may also comprise beads for conducting an immunoprecipitation. Each component of the antibody-based kits is generally in its own suitable container. Thus, these kits generally comprise distinct containers suitable for each antibody. Further, the antibody-based kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.

Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.

EXAMPLES

The following examples are provided for illustrative purposes only and are not intended to limit the scope of the invention.

Example 1

FIG. 4 shows a synthetic scheme useful in preparing 10-propargyl-10-dAM in accordance with the invention. A mixture of 60% NAH in oil dispersion (1.06 g, 26.5 mmol) in 18 mL of sieve-dried THF was cooled to 0° C. The cold mixture was treated with a solution of homoterephthalic acid dimethyl ester (5.0 g, 24 mmol. compound 1 in FIG. 4) in dry THF (7 mL), and the mixture was stirred for 1 hour at 0° C. Propargyl bromide (26.4 mmol) was added, and the mixture was stirred at 0° C. for an additional 1 hour, and then at room temperature for 16 hours. The resulting mixture was treated with 2.4 mL of 50% acetic acid and then poured into 240 mL of water. The mixture was extracted with ether (2.times.150 mL). The ether extracts were combined, dried over Na₂SO₄, and concentrated to an orange-yellow oil. Chromatography on silica gel (600 mL of 230-400 mesh) with elution by cyclohexane-EtOAc (8:1) gave the product α-propargylhomoterephthalic acid dimethyl ester (compound 2) as a white solid (4.66) which appeared by TLC (cyclohexane-EtOAc, 3:1) to be homogeneous. Mass spectral data on this product, however, showed it to be a mixture of the desired product 2, and the dipropargylated compound. No starting material 1 was detected. HPLC shows the ratio of mono- to di-propargylated products to be about 3:1. Since the dipropargylated product, unlike compound 1, cannot produce an unwanted coproduct in the next step of the reaction, this material was suitable for conversion to compound 3. Absence of starting compound 1 in the product used to proceed in the synthesis is very important in order to avoid the sequential formation of 10-dAM during the transformations lading to the final product, because complete removal from 10-dAM from 10-propargyl-1-dAM is very difficult.

A mixture was formed by combining 0.36 g of a 60% NaH (9 mmol) in oil dispersion with 10 mL of dry DMF and cooled to 0-5° C. The cold mixture was treated drop-wise with a solution of the product of the first reaction (compound 2) (2.94 g, 12 mmol) in 10 mL dry DMF and then stirred at 0° C. for 30 minutes. After cooling to −25° C., a solution of 2,4,diamino-6-(bromomethyl)-pteridine hydrobromide-0.2 2-propanol (1.00 g, 2.9 mmol) in 10 mL dry DMF was added drop-wise while the temperature was maintained near −25° C. The temperature of the stirred mixture was allowed to rise to −10° C. over a period of 2 hours. After an additional 2 hours at −10° C., the temperature was allowed to rise to 20° C., stirring at room temperature was continued for 2 hours longer. The reaction was then adjusted to pH 7 by addition of solid CO₂, After concentration in vacuo to remove solvent, the residue was stirred with diethyl ether and the ether insoluble material was collected, washed with water, and dried in vacuo to give 1.49 g of a crude product. This crude product was dissolved in CHCl₃-MeOH (10:1) for application to a silica gel column. Elution by the same solvent system afforded 10-propargyl-10-carbomethoxy-4-deoxy-4-amino-10-deazapteroic acid methyl ester (compound 3) which was homogenous to TLC in 40% yield (485 mg).

A stirred suspension of compound 3 (400 mg, 0.95 mmol) in 2-methoxyethanol (5 mL) was treated with water (5 mL) and then 10% sodium hydroxide solution (3.9 mL). The mixture was stirred as room temperature for 4 hours, during which time solution occurred. The solution was adjusted to pH 8 with acetic acid and concentrated under high vacuum. The resulting residue was dissolved in 15 mL of water and acidified to pH 5.5-5.8 resulting in formation of a precipitate. The precipitate was collected, washed with water and dried in vacuo to recover 340 mg of compound 4 (91% yield). HPLC analysis indicated a product purity of 90%.

Compound 4 (330 mg) was decarboxylated by heating in 15 mL DMSO at 115-120° C. for 10 minutes. A test by HPLC after 10 minutes confirmed that the conversion was essentially complete. DMSO was removed by distillation in vacuo (bath at 40° C.). The residue was stirred with 0.5 N NaOH to give a clear solution, Acidification to pH 5.0 with 1N HCl gave 10-propargyl-4-deoxy-4-amino-10-deazapteroic acid (compound 5) as a yellow solid in 70% yield. HPLC indicated product purity at this stage as 90%.

Compound 5 (225 mg, 0.65 mmol) was coupled with dimethyl L-glutamate hydrochloride (137 mg, 0.65 mmol) using BOP reagent (benzotriazole-1-yloxytris(dimethylamino) phosphonium hexafluorophosphate (287 mg, 0.65 mmol, Aldrich Chemical Co.) in DMF (10 mL) containing triethylamine (148 mg, 1.46 mmol). The mixture was stirred for 3 hours at 20-25° C. and then evaporated to dryness. The residue was stirred with water, and the water-insoluble crude product was collected and dried in vacuo. The crude product (350 mg) was purified by silica gel chromatography with elution by CHCl₃-MeOH (10:1) containing triethylamine (0.25% by volume) to recover 165 mg of 10-propargyl-10-deazaaminopterin dimethyl ester (compound 6, 50% yield) which was homogeneous to TLC (CHCl₃-MeOH 5:1).

Compound 6 (165 mg, 0.326 mmol) was suspended in 10 mL stirred MeOH to which 0.72 mL (0.72 meq) 1N NaOH was added. Stirring at room temperature was continued until solution occurred after a few hours. The solution was kept at 20-25°. for 8 hours, then diluted with 10 mL water. Evaporation under reduced pressure removed the methanol, and the concentrated aqueous solution was left at 20-25° C. for another 24 hours. HPLC then showed the ester hydrolysis to be complete. The clear aqueous solution was acidified with acetic acid to pH 4.0 to precipitate 10-propargyl-10-deazaaminopterin as a pale yellow solid, The collected, water washed and dried in vacuo product weighed 122 mg (79% yield). Assay by elemental analysis, proton NMR and mass spectroscopy were entirely consistent with the assigned structure. HPLC analysis indicated purity of 98% and established the product to be free of 10-deazaaminopterin.

FIG. 3 shows an HPLC of a highly purified preparation consisting essentially of 10-propargyl-10-dAM in accordance with the invention prepared using the method described in Example 1. In this case, the amount of 10-propargyl-10-dAM (as determined by HPLC peak area) approaches 98%, and the peak corresponding to 10-deazaaminopterin is not detected by the processing software although there is a minor baseline ripple in this area.

Example 2

This example describes testing of 10-propargyl-10-dAM and MTX for cytotoxicity against human lymphoma cell lines.

10-propargyl-10-dAM preparation prepared in accordance with Example 1 and an MTX preparation were tested for cytotoxicity against a panel of five human lymphoma cell lines. Experiments were performed as described previously. (Sirotnak et al., Cancer Chemother. Pharmacol. 12: 18-25 (1984). In brief, 2.5 to 5×10³ cells were plated per well in 96-well flat bottom plates. Drug was added in a 0.9% NaCl solution (pH 7.0) over a range of concentrations, and cells were continuously exposed to drug for 5 days. Colorimetric dye (XTT or Alamar blue) was added for an addition period of time (XTT dye, 6 hours, Alamar blue, 24 hours). Each plate was then read on an automated plate reader at 590 nm. The percentage of inhibition was calculated as growth of cells exposed to drug divided by growth of controls (cells incubated with media only). IC₅₀ values were determined as the drug concentrations at which cell growth was inhibited 50% as compared to controls. Experiments were repeated as least three times. Experiments were also conducted with continuous drug exposures lasting for 3 and 4 days with results similar to the 5 day results. The results of the study with 5 day drug exposures is summarized in Table 1. As shown, in every instance, the IC₅₀ of 10-propargyl-10-dAM was substantially lower than the IC₅₀ for MTX, indicating greater potency and/or the ability to use lower and therefore less toxic amounts to achieve the same efficacy.

TABLE 1 Relative growth inhibition in vitro Cell Line Lymphoma Type IC₅₀ PDX (nM) IC₅₀ MTX (nM) Hs445 Hodgkin's disease 1.6 ± 0.8 32 ± 2.2 HT Diffuse large B-cell 2.0 ± 0.4 35 ± 5.0 Raji Burkitt's 2.0 ± 0.3 16 ± 0.8 RL Transformed follicular 23.0 ± 2.0  210 ± 40   SKI-DLCL-1 Diffuse large B-cell 5.1 ± 0.1 48 ± 2.5

Example 3

This example describes the effects of 10-propargyl-10-dAM used in a Phase I/II study on T-cell lymphomas.

In this study, patients with aggressive lymphoma were enrolled, including three patients with drug-resistant T-cell lymphoma. The following case summaries have been obtained. Each of these patients was also treated with folic acid (1 mg/m² daily starting 1 week prior to treatment with 10-propargyl-10-dAM) and Vitamin B₁₂ (1 mg/mg/m² monthly) supplementation.

Patient 1 had a diagnosis of Peripheral T-cell Lymphoma, Stage 1V. Demographics: 48 Year old male; Prior Treatment: CHOP.times.4 cycles (July 2002-November 2002) refractory, ICE.times.2 cycles (December 2002) refractory, Campath (March 2003-June 2003)—mixed response; Pre-Treatment Staging: Extensive disease cutaneous disease. Treatment on Study: 10-propargyl-10-dAM 135 mg/m² times.1 dose. Toxicitics observed were Grade 3 stomatitis; neutropenia grade 3; sepsis; Response: Essentially complete remission by PET scan. Comment: This patient ultimately died after developing a bacteremia and sepsis from open skin lesions with Gram positive bacteria.

Patient 2 had a diagnosis of Lymphoblastic Lymphoma, Precursor T-cell, Stage 1V. Demographics: 65 year old female; Prior Treatment: L20—Complex combination chemotherapy since May 2002, administered over two years. Has received MTX from May 2002 through February 2004. Relapsed December 2004. Pre-Treatment Staging: Extensive widespread relapse. Treatment on Study: 10-propargyl-10-dAM 30 mg/m² 2.times.3 weeks every 4 weeks. Completed 3 cycles to date. Toxicities: None Response: Complete remission by PET and CT. Comment: Patient with essentially methotrexate resistant disease with extensive sinus based disease which began resolving after one dose of 10-propargyl-10-dAM. Patient 3 had a diagnosis of HTLV Associated T-cell Lymphoma. Demographics: 38 Year old male; Prior Treatment: EPOCH—infusional combination chemotherapy October 2003 to February 2004. Pre-Treatment Staging: Left axillary disease. Treatment on Study: 10-propargyl-10-dAM 30 mg/m² weekly.times.3 every 4 weeks.times.2 cycles; Toxicities: None. Response: Complete remission. Comment: Complete disappearance of clinically evident disease by the end of the first cycle, very well tolerated, no toxicity. Patient 4 had a diagnosis of Panniculitic T-cell Lymphoma. Demographics: 25 Year old male; Prior Treatment: Ontak (refractory), September 2002-November 2002; Targretin and IFN .alpha. January 2003-October 2003 (durable partial remission); CHOP April 2004-June 2004; ICE June 2004, CyPen July 2004-August 2004, Targretin/MTX September 2004 to February 2005; Treatment on Study: 10-propargyl-10-dAM 30 mg/m² weekly.times.4. Response: Clinical complete remission by PET; Toxicities: None; Comment: healing subcutaneous lesions, too numerous to count, large ulcerative granulating lesion.

This Example shows that the 4 patients with T-cell lymphoma treated with 10-propargyl-1,0-dAM in this example have all met criteria for complete remission, even based on the sensitive PET imaging techniques. Interestingly, the patient treated at 135 mg/m² received only a single dose of drug with a dramatic response to therapy, while the others had received only small modest doses on a weekly schedule.

Example 4

This example describes the effects of 10-propargyl-10-dAM on lymphoma growth in vivo.

Subcutaneous transplantation models in NOD/SCID mice were generated using three established human lymphoma cell line representative of aggressive transformed FL (RL) and de novo extranodal DLBCL (HT; SKI-DLCL-I) histologies. Methods are described in Wang et al., Leukemia and Lymphoma, 2003, Vol. 44 (6), pages 1027-1035 and Rots et al. Leukemia 14:2166-2175 (2000). Six to eight week old non-obese diabetic severe combined immunodeficient (NOD/SCID) mice (Jackson Laboratories, Bar Harbor, Me.) were sub-lethally irradiated with three cGy from a gamma source and inoculated with 10×10⁶ lymphoma cells via a subcutaneous route. When tumor volumes approached 100 mm³, mice were divided into three groups, averaging 3-8 mice per group. Mice were treated with normal saline or the maximum tolerated dose (MTD) of MTX (40 mg/kg) or 10-propargyl-10-dAM (60 mg/kg) via an intraperitoneal route twice weekly for two weeks (four total doses). The MTD of each drug has been previously shown to result in less than 10% weight loss and no toxic deaths in nude mice. (Sirotnak, et al., Cancer Chemother. Pharmacol. 12: 26-30 (1984); Sirotnak et al., Cancer Chemother. Pharmacol. 42: 313-318 (1998). Engraftment rates in this experiment ranged from 80 to 90%. Palpable tumors formed under the skin approximately 7-10 days after inoculation and were readily measurable with calipers. Mice with subcutaneous lymphoma growths survived an average of 40-50 days after inoculation. Treatment results in lymphoma xenografted mice are summarized in Tables 2-4. As shown in Table 2 and 3, in the RL (transformed FL) and SKI-DLCL-I xenografts, 10-propargyl-10-dAM treatment resulted in much greater inhibition of lymphoma growth than MTX. These tumors were only minimally sensitive to MTX treatment with small reductions in growth an no regressions. 10-propargyl-10-dAM treatment, however, decreased tumor volumes by at least 50% from initial volumes and induced tumor regressions in 57% (5 of 9 mice) and 30% (3 of 10 mice) of RL and SKI-DLCL-I, respectively.

TABLE 2 Treatment of human RL (transformed follicular) non-Hodgkin's lymphoma xenografts. Avg Avg Change in Weight Tumor Tumor Tumor Complete Dose Change Diameter Volume Regression Regression Agent (mg/kg) (%) (mm ± SE) (mm ± SE) (%) (no/total) Control — +15.9 12.5 ± 1.3 +1228 ± 238  — 0/7 MTX 40 −14.8 10.9 ± 0.5 +619 ± 108 —  0/12 PDX 60 −11.1  2.7 ± 1.1 −46 ± 34 56 5/9

TABLE 3 Treatment of human SKI-DLCL-1 (de novo diffuse large B-cell) non-Hodgkin's lymphoma xenografts Avg Avg Change in Weight Tumor Tumor Tumor Complete Dose Change Diameter Volume Regression Regression Agent (mg/kg) (%) (mm ± SE) (mm ± SE) (%) (no/total) Control — +4.9  12 ± 0.3 +786 ± 64 — 0/8  MTX 40 −1.9 9.5 ± 0.4 +299 ± 58 — 0/10 PDX 60 −1.2 3.5 ± 0.7  −81 ± 16 54 3/10

As shown in Table 4, even more significant results were achieved using 10-propargyl-10-dAM in the treatment of HT xenografts. Although MTX treatment resulted in modest growth inhibition as compared to controls, there was no tumor regression in these animals. In contrast, 10-propargyl-10-dAM administration resulted in complete tumor regression in 89% (8 of 9) of the mice with an average tumor regression of 99%. At the nadir of tumor regression, HL xenograft mice treated with 10-propargyl-10-dAM had an average tumor diameter of 0.5 mm, as opposed to 11.2 mm for the control and 8.7 mm for MDX-treated mice.

TABLE 4 Treatment of human HT (diffuse large B-cell) non-Hodgkin's lymphoma xenografts. Avg Avg Change in Weight Tumor Tumor Tumor Complete Dose Change Diameter Volume Regression Regression Agent (mg/kg) (%) (mm ± SE) (mm ± SE) (%) (no/total) Control — +13.2 11.2 ± 1.3  641 ± 252 — 0/8 MIX 40 −9.8 8.7 ± 2.0 +300 ± 225  — 0/7 PDX 60 −8.9 0.5 ± 0.3 −95 ± 0.8  99 8/9

Example 5

This example describes relative expression of selected genes in B- and T-cell lymphoma cell lines.

Several proteins are implicated in the metabolism of folic acid and targets for anti-folates in tumor cells. In most tumor cells, the protein encoded by RFC-1 mediates internalization of folate analogs. Once inside the cell, these analogs either bind dihydrofolate reductase (DHFR), thereby depleting intracellular reduced folate pools needed for purine and thymidine biosynthesis, or will be metabolized to a polyglutamate prior to binding to DHFR. Polyglutamylation is catalyzed by FPGS. FPGH mediates cleavage and clearance of these intracellular polyglutamated anti-folates. Using quantitative RT-PCR techniques, expression levels were determined in RL, HT and SKI-DCBCL-I cell lines for RFC-1, FPGS and FPGH using primers and methods as described in Wang et al., Leukemia and Lymphoma, 2003, Vol. 44 (6), pages 1027-1035 and Rots et al. Leukemia 14:2166-2175 (2000). The results of these determinations are summarized in Table 5. As shown, the HT cell line, which was most sensitive to 10-propargyl-10-dAM, also had the greatest levels of RFC-1 expression both on an absolute level and relative to FPGS while the levels of RFC-1 for SKI-DCBCL-I and RL, which had similar sensitivity to 10-propargyl-10-dAM, are similar to one another. Without intending to be bound by a specific mechanism, it is believed that this correlation between RFC-1 expression levels and 10-propargyl-10-dAM sensitivity is a reflection of increased transport of 10-propargyl-10-dAM into tumor cells.

TABLE 5 Relative levels of RFC-1, FPGS, and FPGH mRNA gene expression in lymphoma cell lines as determined by real-time RT-PCR. RFC-1 FPGS FPGH Cell (n = 5) (n = 5) (n = 5) HT 0.96 ± 0.2 4.92 ± 0.6 1.06 ± 0.2  SKI-DCBCL-I  0.30 ± 0.04 6.84 ± 0.6 1.08 ± 0.10 RL 0.41 ± 0.1 7.28 ± 0.8 0.58 ± 0.08

Example 6

This example describes relative expression of selected genes in B- and T-cell lymphoma cell lines.

Using quantitative RT-PCR techniques, expression levels were determined in RL and HT cell lines for DHFR, GARFT, GGH, TS, RFC-1, and FPGS using primers and methods described in Wang et al., Leukemia and Lymphoma, 2003, Vol. 44 (6), pages 1027-1035 and Rots et al. Leukemia 14:2166-2175 (2000). See FIG. 5( a)-(f). Results show that in particular, median expression of RFC-1 and TS trended higher in the T-cell lymphoma cell line than in the B-cell lymphoma cell line. Together with the data showing greater sensitivity of T-cell lymphoma lines to 10-propargyl-10-dAM treatment than B-cell lymphoma lines (including Example 3), these results suggest that T-cell lymphomas' observed greater susceptibility to treatment with 10-propargyl-10-dAM is related to enzymes of the folate pathway and includes differential expression of these enzymes in T-cell lymphomas. Such proteins include DHFR, GARFT, GGH, TS, RFC-1, FPGS, and particularly RFC-1 and TS.

Example 7

This example describes a comparison of relative gene expression of selected folate pathway genes during treatment of B-cell (RL) and T-cell (HT) lymphoma cells with 10-propargyl-10-dAM and MTX.

A 10-propargyl-10-dAM preparation prepared in accordance with Example 1 and an MTX preparation were tested for cytotoxicity against a representative B-cell human lymphoma cell lines (RL) and T-cell (HT) human lymphoma cell line. Experiments were performed as described previously. (Sirotnak et al., Cancer Chemother. Pharmacol. 12: 18-25 (1984). In brief, 2.5 to 5×10³ cells were plated per well in 96-well flat bottom plates. Drug was added in a 0.9% NaCl solution (pH 7.0) with either 1 nM or 50 nM of 10-propargyl-10-dAM and MTX and gene expression of selected folate pathway enzymes was quantified by RT-PCR as discussed previously at time 0, 1 hour post-treatment, and 12 hours post treatment. Relative enzyme expression levels were determined for reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH) (also known as folypolyglutamate hydrolase (FPGH)), folylpoly-gamma-glutamate synthetase (FPGS), and glycinamide ribonucleotide formyltransferase (GARFT) was measured at time 0, at 1 hour, and at 12 hours post-treatment. See FIGS. 6( a)-(f). Ct refers to “cycle threshold” and refers to the number of PCR cycles required to generate enough product for the specific antibody to the target. Actin is used as an internal reference. The expression of the selected polypeptide is expressed as relative to actin.

Results show that RFC-1 expression is several-fold (approximately 7-fold) higher for T-cell (H9) than for B-cell (RL) cell lines and that treatment with low-dose 10-propargyl-10-dAM causes a rapid induction of RFC-1. Results also show that DHFR expression is similar in T-cell (H9) and B-cell (RL) cell lines, and is upregulated, followed by down-regulation, upon treatment of MTX and 10-propargyl-10-dAM. Results show that FPGS expression is similar in T-cell (H9) and B-cell (RL) cell lines, and low dose 10-propargyl-10-dAM produces a rapid two fold induction of FPGS. Results also show that TS expression is seven fold higher in T-cell (H9) than B-cell (RL) cell lines, with upregulation followed by downregulation upon treatment with MTX and 10-propargyl-10-dAM. Further, the results show that GARFT expression is two fold higher in T-cell (H9) than B-cell (RL) and is downregulated upon treatment with 10-propargyl-10-dAM and MTX; and that GGH expression is similar in T-cell (H9) and B-cell (RL) cell lines, with upregulation and downregulation of expression seen upon treatment with 10-propargyl-10-dAM and MTX.

Example 8

This example describes relative expression of selected genes in B- and T-cell lymphoma cell lines and in a multiple myeloma cell line.

Using quantitative RT-PCR techniques, expression levels were determined in a number of cell lines for DHFR, GARFT, GGH, TS, RFC-1, and FPGS using primers described in Rots et al. Leukemia 14:2166-2175 (2000), including SKI (B-cell lymphoma line), H9 (T-cell lymphoma line), CCL119 (T-cell lymphoma line), TIB152 (T-cell lymphoma line), RL (B-cell lymphoma line), HPB ALL (T-cell lymphoma line), JJN3 (multiple myeloma cell line), Pl2lchikawa (T-cell lymphoma cell line), Ly1 (B-cell lymphoma line), and CUTLL1 (T-cell lymphoma line). See Table 6. Results show that in particular, median expression of RFC-1 and TS in particular trended higher in the multiple myeloma cell line JJN3. Together with the data showing greater sensitivity of T-cell lymphoma lines to 10-propargyl-10-dAM treatment than B-cell lymphoma lines (including Example 3) and higher RFC-1 expression, these results show that multiple myeloma may have greater susceptibility to treatment with 10-propargyl-10-dAM, and that biomarkers for such sensitivity may include DHFR, GARFT, GGH, TS, RFC-1, AND FPGS, and RFC-1 and TS.

TABLE 6 PDX Cell Line Untreated RT-PCR Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct DHFR Ct DeltaCt A SKI AGR-06-0002291 28.07 21.71 22.84 5.23 B H9 AGR-06-0002292 30.48 8.72 23.94 6.54 C CCL119 AGR-06-0002293 29.69 9.33 23.24 6.45 D TIB 152 AGR-06-0002294 30.33 16.06 24.66 5.66 E RL AGR-06-0002295 27.29 12.04 21.22 6.08 F HPB ALL AGR-06-0002296 29.71 17.64 24.18 5.53 G JJN3 AGR-06-0002297 30.60 32.52 25.96 4.64 H Pl21chikawa AGR-06-0002298 30.07 16.39 24.44 5.63 I Ly1 AGR-06-0002299 31.77 10.30 25.47 6.30 J CUTLL1 AGR-06-0002300 32.67 10.19 26.35 6.32 Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct FPGS Ct DeltaCt A SKI AGR-06-0002291 29.83 0.44 22.84 6.99 B H9 AGR-06-0002292 31.24 0.35 23.94 7.31 C CCL119 AGR-06-0002293 30.97 0.26 23.24 7.72 D TIB 152 AGR-06-0002294 31.30 0.55 24.66 6.64 E RL AGR-06-0002295 29.16 0.22 21.22 7.95 F HPB ALL AGR-06-0002296 31.34 0.39 24.18 7.16 G JJN3 AGR-06-0002297 33.09 0.40 25.96 7.13 H P121chikawa AGR-06-0002298 31.89 0.32 24.44 7.45 I Ly1 AGR-06-0002299 33.57 0.20 25.47 8.10 J CUTLL1 AGR-06-0002300 33.56 0.37 26.35 7.21 Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct GARFT Ct DeltaCt A SKI AGR-06-0002291 29.26 1.55 22.84 6.42 B H9 AGR-06-0002292 29.97 2.02 23.94 6.04 C CCL119 AGR-06-0002293 30.18 1.09 23.24 6.93 D TIB 152 AGR-06-0002294 30.83 1.84 24.66 6.17 E RL AGR-06-0002295 27.92 1.27 21.22 6.70 F HPB ALL AGR-06-0002296 30.72 1.43 24.18 6.54 G JJN3 AGR-06-0002297 31.46 2.93 25.96 5.50 H P121chikawa AGR-06-0002298 31.14 1.28 24.44 6.70 I Ly1 AGR-06-0002299 31.83 1.62 25.47 6.36 J CUTLL1 AGR-06-0002300 33.73 0.79 26.35 7.38 Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct GGH Ct DeltaCt A SKI AGR-06-0002291 30.27 0.82 22.69 7.58 B H9 AGR-06-0002292 31.81 0.61 23.80 8.01 C CCL119 AGR-06-0002293 31.02 0.66 23.14 7.89 D TIB 152 AGR-06-0002294 32.15 0.81 24.54 7.61 E RL AGR-06-0002295 29.21 0.61 21.20 8.00 F HPB ALL AGR-06-0002296 31.86 0.73 24.11 7.75 G JJN3 AGR-06-0002297 28.68 23.16 25.92 2.76 H P121chikawa AGR-06-0002298 32.79 0.48 24.45 8.34 I Ly1 AGR-06-0002299 33.39 0.61 25.39 8.00 J CUTLL1 AGR-06-0002300 34.15 0.67 26.28 7.87 Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct RFC1 Ct DeltaCt A SKI AGR-06-0002291 30.75 1.91 22.69 8.07 B H9 AGR-06-0002292 30.15 6.25 23.80 6.35 C CCL119 AGR-06-0002293 30.49 3.12 23.14 7.36 D TIB 152 AGR-06-0002294 31.45 4.27 24.54 6.90 E RL AGR-06-0002295 29.90 1.24 21.20 8.69 F HPB ALL AGR-06-0002296 31.19 3.79 24.11 7.08 G JJN3 AGR-06-0002297 31.77 8.82 25.92 5.86 H P121chikawa AGR-06-0002298 31.26 4.56 24.45 6.81 I Ly1 AGR-06-0002299 32.25 4.40 25.39 6.86 J CUTLL1 AGR-06-0002300 32.70 6.01 26.28 6.41 Allos Sam- ple Num- COM- Actin ber MENTS RGI Accession Ct TS Ct DeltaCt A SKI AGR-06-0002291 28.48 5.26 22.69 5.80 B H9 AGR-06-0002292 28.09 14.94 23.80 4.29 C CCL119 AGR-06-0002293 27.23 17.13 23.14 4.10 D TIB 152 AGR-06-0002294 27.56 36.18 24.54 3.02 E RL AGR-06-0002295 27.49 3.75 21.20 6.29 F HPB ALL AGR-06-0002296 27.64 25.37 24.11 3.53 G JJN3 AGR-06-0002297 28.29 56.71 25.92 2.37 H P121chikawa AGR-06-0002298 27.95 25.97 24.45 3.50 I Ly1 AGR-06-0002299 30.59 7.97 25.39 5.20 J CUTLL1 AGR-06-0002300 29.70 27.50 26.28 3.41

The foregoing discussion of the invention has been presented for purposes of illustration and description. The foregoing is not intended to limit the invention to the form or forms disclosed herein. Although the description of the invention has included description of one or more embodiments and certain variations and modifications, other variations and modifications are within the scope of the invention, e.g., as may be within the skill and knowledge of those in the art, after understanding the present disclosure. It is intended to obtain rights which include alternative embodiments to the extent permitted, including alternate, interchangeable and/or equivalent structures, functions, ranges or steps to those claimed, whether or not such alternate, interchangeable and/or equivalent structures, functions, ranges or steps are disclosed herein, and without intending to publicly dedicate any patentable subject matter. 

1. A method of selecting a patient for treatment of a cancer with 10-propargyl-10-deazaaminopterin, the method comprising the steps of: (a) obtaining a sample of the patient's cancer tissue; (b) determining the expression level of at least one selected polypeptide expressed by the sample; (c) obtaining a reference expression level for the at least one selected polypeptide for a cancer having sensitivity to 10-propargyl-10-deazaaminopterin; (d) comparing the expression data for the at least one selected polypeptide of step (b) with the reference expression for the at least one selected polypeptide of step (c), wherein a match of the sample expression of the at least one selected polypeptide to the reference expression of the at least one selected polypeptide indicates the patient's cancer has greater sensitivity to 10-propargyl-10-deazaaminopterin, wherein the at least one selected polypeptide is selected from the group consisting of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT); and (e) selecting the patient for treatment 10-propargyl-10-deazaaminopterin when the expression of the at least one sample polypeptide and the at least one reference polypeptide matches.
 2. The method of claim 1, wherein the reference cancer is a T-cell lymphoma, a NSCLC, or a multiple myeloma.
 3. The method of claim 1, wherein the at least one selected polypeptide is RFC-1.
 4. The method of claim 1, wherein the at least one selected polypeptide is TS.
 5. The method of claim 1, wherein the at least one selected polypeptide is DHFR.
 6. The method of claim 1, wherein a match is defined as the at least one selected polypeptide having an expression level of at least 50% of the reference's at least one selected polypeptide expression level.
 7. The method of claim 1, wherein the patient's cancer is lymphoma, multiple myeloma, or NSCLC.
 8. The method of claim 7, wherein the lymphoma is a T-cell lymphoma selected from the group consisting of lymphoblastic lymphomas in which the malignancy occurs in primitive lymphoid progenitors from the thymus; mature or peripheral T-cell neoplasms, including T-cell prolymphocytic leukemia, T-cell granular lymphocytic leukemia, aggressive NK-cell leukemia, cutaneous T-cell lymphoma (Mycosis fungoides/Sezary syndrome), anaplastic large cell lymphoma, T-cell type, enteropathy-type T-cell lymphoma, Adult T-cell leukemia/lymphoma including those associated with HTLV-1, and angioimmunoblastic T-cell lymphoma, and subcutaneous panniculitic T-cell lymphoma; and peripheral T-cell lymphomas that initially involve a lymph node paracortex.
 9. A method for assessing sensitivity of a patient's cancer to treatment with 10-propargyl-10-deazaaminopterin comprising the steps of: (a) obtaining a sample of the patient's cancer tissue; (b) determining the expression level of at least one selected polypeptide expressed by the sample; (c) obtaining a reference expression level for the at least one selected polypeptide for a least one cancer having sensitivity to 10-propargyl-10-deazaaminopterin; (d) comparing the expression data for the at least one selected polypeptide of step (b) with the reference expression for the at least one selected polypeptide of step (c), wherein a match of the sample expression level of the at least one selected polypeptide to the reference expression level of the at least one selected polypeptide indicates the patient's cancer has greater sensitivity to 10-propargyl-10-deazaaminopterin, wherein the at least one selected polypeptide is selected from the group consisting of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT); and (e) generating a report of the sensitivity of the sample to 10-propargyl-10-deazaaminopterin.
 10. The method of claim 9, wherein the reference cancer is a T-cell lymphoma, NSCLC, or multiple myeloma.
 11. The method of claim 9, wherein the at least one selected polypeptide is RFC-1.
 12. The method of claim 9, wherein the at least one selected polypeptide is TS.
 13. The method of claim 9, wherein the at least one selected polypeptide is DHFR.
 14. The method of claim 9, wherein a match is defined as the at least one selected polypeptide having an expression level of at least 50% of the reference's at least one selected polypeptide expression level.
 15. The method of claim 9, wherein the patient's cancer is lymphoma, NSCLC, or multiple myeloma.
 16. The method of claim 15, wherein the lymphoma is a T-cell lymphoma selected from the group consisting of lymphoblastic lymphomas in which the malignancy occurs in primitive lymphoid progenitors from the thymus; mature or peripheral T-cell neoplasms, including T-cell prolymphocytic leukemia, T-cell granular lymphocytic leukemia, aggressive NK-cell leukemia, cutaneous T-cell lymphoma (Mycosis fungoides/Sezary syndrome), anaplastic large cell lymphoma, T-cell type, enteropathy-type T-cell lymphoma, Adult T-cell leukemia/lymphoma including those associated with HTLV-1, and angioimmunoblastic T-cell lymphoma, and subcutaneous panniculitic T-cell lymphoma; and peripheral T-cell lymphomas that initially involve a lymph node paracortex.
 17. A method for the treatment of multiple myeloma comprising administering to a patient diagnosed with having multiple myeloma a pharmaceutically acceptable composition comprising a therapeutically effective amount of 10-propargyl-10-deazaaminopterin.
 18. The method of claim 17, wherein the 10-propargyl-10-deazaaminopterin is substantially free of 10-deazaaminopterin.
 19. The method of claim 17, wherein the 10-propargyl-10-deazaaminopterin is administered in an amount of from about 30 to about 275 mg/m² per dose.
 20. A method to modulate the expression of a polypeptide in a patient's cancer comprising administering to the patient an effective amount of 10-propargyl-10-deazaaminopterin, wherein the polypeptide is selected from the group consisting of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT).
 21. The method of claim 20, wherein the patient has lymphoma, multiple myeloma, or NSCLC.
 22. The method of claim 20, wherein the modulation is down-regulation and the polypeptide is TS or DHFR.
 23. The method of claim 20, wherein the 10-propargyl-10-deazaaminopterin is substantially free of 10-deazaaminopterin.
 24. The method of claim 20, wherein the 10-propargyl-10-deazaaminopterin is administered in an amount of from about 30 to about 275 mg/m² per dose.
 25. The method of claim 20, wherein the polypeptide is RFC-1.
 26. A kit for assessing sensitivity of a patient's cancer to treatment with 10-propargyl-10-deazaaminopterin comprising at least two sets of selected polypeptide RNA-specific primers wherein each set of specific primers produces double stranded DNA complementary to at least one selected polypeptides, wherein each first primers of said sets contains a sequence which can selectively hybridize to RNA, cDNA or an EST complementary to one of the selected polypeptides to create an extension product and each said second primers of said sets is capable of selectively hybridizing to said extension product, wherein the at least one selected polypeptide is selected from the group consisting of reduced folate carrier-1 enzyme (RFC-1), dihydrofolate reductase (DHFR), folylpoly-gamma-glutamate synthetase (FPGS), thymidylate synthase (TS), γ-glutamyl hydrolase (GGH), and glycinamide ribonucleotide formyltransferase (GARFT).
 27. The kit of claim 26, wherein the at least one selected peptide is RFC-1. 